X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FMouseOverStructureListener.java;h=78f383ad34eb588632664f1a55e92afca23f4336;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=c1d3a402deb39cd02dff981c906f119db8266229;hpb=362f2db1b01f3562784864a1d6ac5f7b9be0a18a;p=jalview.git
diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index c1d3a40..78f383a 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -1,264 +1,324 @@
-package jalview.javascript;
-
-import java.awt.Color;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.appletgui.AlignFrame;
-import jalview.bin.JalviewLite;
-import jalview.datamodel.SequenceI;
-import jalview.ext.jmol.JmolCommands;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-
-public class MouseOverStructureListener extends JSFunctionExec implements
- JsCallBack, StructureListener
-{
-
- String _listenerfn;
-
- String[] modelSet;
-
- public MouseOverStructureListener(JalviewLite jalviewLite,
- String listener, String[] modelList)
- {
- super(jalviewLite);
- _listenerfn = listener;
- modelSet = modelList;
- if (modelSet != null)
- {
- for (int i = 0; i < modelSet.length; i++)
- {
- // resolve a real filename
- try
- {
- if (new java.net.URL(modelSet[i]).openConnection() != null)
- {
- continue;
- }
- } catch (Exception x)
- {
- }
- ;
- try
- {
- String db = jvlite.getDocumentBase().toString();
- db = db.substring(0, db.lastIndexOf("/"));
- if (new java.net.URL(db + "/" + modelSet[i]).openConnection() != null)
- {
- modelSet[i] = db + "/" + modelSet[i];
- continue;
- }
- } catch (Exception x)
- {
- }
- ;
- try
- {
- if (new java.net.URL(jvlite.getCodeBase() + modelSet[i])
- .openConnection() != null)
- {
- modelSet[i] = jvlite.getCodeBase() + modelSet[i];
- continue;
- }
- } catch (Exception x)
- {
- }
- ;
-
- }
- }
- }
-
- @Override
- public String[] getPdbFile()
- {
- return modelSet;
- }
-
- @Override
- public void mouseOverStructure(int atomIndex, String strInfo)
- {
-
- // StructureSelectionManager.getStructureSelectionManager().mouseOverStructure(atomIndex,
- // chain, pdbfile)
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbId)
- {
- String[] st = new String[0];
- try
- {
- executeJavascriptFunction(_listenerfn, st = new String[]
- { "mouseover", "" + pdbId, "" + chain, "" + (pdbResNum),
- "" + atomIndex });
- } catch (Exception ex)
- {
- System.err.println("Couldn't execute callback with " + _listenerfn
- + " using args { " + st[0] + ", " + st[1] + ", " + st[2]
- + "," + st[3] + "\n");
- ex.printStackTrace();
-
- }
-
- }
-
- @Override
- public synchronized void updateColours(Object srce)
- {
- final Object source = srce;
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(jvlite);
- // if (jvlite.debug)
- // {
- // ssm.reportMapping();
- // }
- if (source instanceof jalview.api.AlignmentViewPanel)
- {
- SequenceI[][] sequence = new SequenceI[modelSet.length][];
- for (int m = 0; m < modelSet.length; m++)
- {
- StructureMapping[] sm = ssm.getMapping(modelSet[m]);
- if (sm != null && sm.length > 0)
- {
- sequence[m] = new SequenceI[sm.length];
- for (int i = 0; i < sm.length; i++)
- {
- sequence[m][i] = sm[i].getSequence();
- }
- }
- else
- {
- sequence[m] = new SequenceI[0];
- }
- // if (jvlite.debug)
- // {
- // System.err.println("Mapped '" + modelSet[m] + "' to "
- // + sequence[m].length + " sequences.");
- // }
- }
-
- SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
- .getSequenceRenderer();
- FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
- .getShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
- ((jalview.appletgui.AlignmentPanel) source).av) : null;
- if (fr != null)
- {
- ((jalview.appletgui.FeatureRenderer) fr)
- .transferSettings(((jalview.appletgui.AlignmentPanel) source)
- .getFeatureRenderer());
- }
- ;
-
- // Form a colour command for the given alignment panel
- final String[] colcommands = JmolCommands.getColourBySequenceCommand(
- ssm, modelSet, sequence, sr, fr,
- ((AlignmentViewPanel) source).getAlignment());
- if (colcommands==null)
- {
- //
- return;
- }
- String mclass,mhandle;
- if (jvlite.isJsMessageSetChanged(mclass="colourstruct",mhandle=((jalview.appletgui.AlignmentPanel) source).av
- .getViewId(), colcommands)) {
- jvlite.setJsMessageSet(mclass, mhandle , colcommands);
- // and notify javascript handler
- String st[] = new String[]
- {
- "colourstruct",
- ""
- + ((jalview.appletgui.AlignmentPanel) source).av
- .getViewId(), ""+colcommands.length, ""+(colcommands[0]!=null ? colcommands[0].length() : 0)};
- try
- {
- executeJavascriptFunction(
- true,
- _listenerfn,st
-);
- } catch (Exception ex)
- {
- System.err.println("Couldn't execute callback with "
- + _listenerfn + " using args { " + st[0] + ", "
- + st[1] + ", " + st[2] + "," + st[3] + "\n");
- ex.printStackTrace();
-
- }
- }
-/* new Thread(new Runnable()
- {
- public void run()
- {
- // and send to javascript handler
- String st[] = new String[0];
- int i = 0;
- for (String colcommand : colcommands)
- {
- // do sync execution for each chunk
- try
- {
- executeJavascriptFunction(
- false,
- _listenerfn,
- st = new String[]
- {
- "colourstruct",
- ""
- + ((jalview.appletgui.AlignmentPanel) source).av
- .getViewId(), handle, "" });
- } catch (Exception ex)
- {
- System.err.println("Couldn't execute callback with "
- + _listenerfn + " using args { " + st[0] + ", "
- + st[1] + ", " + st[2] + "," + st[3] + "\n");
- ex.printStackTrace();
-
- }
- }
- }
- }).start();
- */
- }
-
- }
-
- @Override
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbId)
- {
- return null;
- }
-
- @Override
- public AlignFrame getAlignFrame()
- {
- // associated with all alignframes, always.
- return null;
- }
-
- @Override
- public String getListenerFunction()
- {
- return _listenerfn;
- }
-
- public void finalise()
- {
- jvlite=null;
- super.finalize();
- }
- @Override
- public void releaseReferences(Object svl)
- {
-
- // TODO Auto-generated method stub
-
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
+ * ['mouseover',String(pdb file URI), String(pdb file chain ID), String(residue + * number moused over), String(atom index corresponding to residue)] + *+ * + *
+ * ['colourstruct',String(alignment view id),String(number of javascript message + * chunks to collect),String(length of first chunk in set of messages - or zero + * for null message)] + *+ * + *